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Programming Languages

Expertise: Python, Bash scripting, R and Rstudio, Git/Github, Markdown/Rmarkdown
Familiarity: TypeScript, HTML/CSS, C (Arduino)


Languages

Spanish - Native
English - IELTS 7.0 (CEFR C1)
German - Goethe-Zertifikat A1

Disclaimer

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Last updated on 2024-08-30.

Main

Marisol Navarro-Miranda

Master’s student at Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV), Unidad Irapuato. Microbial Ecology: Bacterial adaptations to extreme environments and Competitive interactions within environmental isolates | Bioinformatics: Comparative genomics and Complex network analysis | Molecular Biology and Microbiology techniques: DNA extraction, PCR, Gel electrophoresis, Microbial cell cultures, Growth kinetics, and Bacterial interaction experiments.

Education

M.Sc., Integrative Biology

Centro de Investigacion y de Estudios Avanzados del IPN (CINVESTAV), Irapuato

Guanajuato, Mexico

current - 2021

  • Ph.D. Gabriela Olmedo-Álvarez and Ph.D. Maribel Hernández-Rosales
  • Thesis: Understanding the genomic basis of antagonistic pairwise interactions in microbial communities
  • Grade: 9.5/10.

B.Sc., Biology

Universidad Nacional Autónoma de México (UNAM), Facultad de Ciencias

Mexico City, Mexico

2019 - 2014

  • Ph.D. Manuel García-Ulloa Gámiz and Ph.D. Valeria Souza Saldivar
  • Thesis: Pangenomic characterization of the bacterial genus Virgibacillus associated with saline habitats
  • Grade: 8.5/10.

Research Experience

Research Internship (Short-term)

Bioinformatics and Agrogenomics Group, Franco-Argentine International Centre for Information and Systems Sciences (CIFASIS), CONICET

Rosario, Argentina

2023

  • Ph.D. Elizabeth Tapia-Centro and Ph.D. Flavio Spetale
  • Project: Machine Learning methods for the prediction of microbial competitive interactions
  • Description: Machine learning methos in R

National Research Assistant Level III, CONACYT

Laboratory of Molecular and Experimental Evolution, Institute of Ecology, UNAM

Mexico City, Mexico

2020 - 2019

  • Ph.D. Valeria Souza Saldivar
  • Project: Describing and explaining the permanence of ancestral marine lineages of microbial mats in Cuatro Ciénegas, Coahuila
  • Description: Fieldwork sampling, mesocosm experiments, and analyze (16S rRNA) metabarcoding data.

Research Internship (Long-term)

University Unit of Massive Throughput Sequencing and Bioinformatics (UUSMB), Institute of Biotechnology (IBt), UNAM

Morelos, Mexico

2017 - 2016

  • M.Sc. Verónica Jiménez-Jacinto
  • Project: Sequencing strategy and genomic analysis of the marine parasite Cymothoa exigua
  • Description: Sequencing strategies for non-model organisms, Programming: Perl, Python, R and Bash, and use of specialized software for NGS data.

Research Internship (Long-term)

Department of Chemical Evolution, Institute of Nuclear Sciences (ICN), UNAM

Mexico City, Mexico

2016 - 2015

  • Ph.D. Alejandro Heredia Barbero
  • Project: Adsorption of histidine exposed to ultraviolet radiation in the presence of Aragonite (CaCO3): An experimental model for prebiotic chemistry
  • Description: UV-VIS spectroscopy analysis, data analysis with Origin Lab, Programming: R, Python, and development of a new methodological strategy for amino acids irradiation.

Research Internship (Short-term)

Department of Plasma Physics, Laboratory of Plasma Chemistry and Planetary Studies, Institute of Nuclear Sciences (ICN), UNAM

Mexico City, Mexico

2015

  • Ph.D. Rafael Navarro González
  • Project: Effect of ionizing radiation on calcium sulfates. Possible applications on the surface of Mars

Research Internship (Short-term)

Genotoxicology and Environmental Mutagenesis Group, Institute of Atmospheric Sciences (CCA), UNAM

Mexico City, Mexico

2014

  • Ph.D. María Elena Calderón Segura
  • Project: Genotoxicological analysis of a keto-enol pesticide in human peripheral lymphocytes by micronucleus assay

Research Internship (Long-term)

Jóvenes Hacia la Investigación in collaboration with the Botanical Garden and Plant Tissue Culture Laboratory of the Biology Institute (IB), UNAM

Mexico City, Mexico

2014 - 2013

  • Ph.D. Víctor Manuel Chávez Ávila and Ph.D. Paulina Heredia Guzmán
  • Project: In vitro culture of Prosthechea vitellina (Orchidaceae)




Teaching Experience

Workshop: Bacterial Genome Mining

Assistant in the International Workshop of Bioinformatics (TIB 2024)

Virtual, International

2024

Workshop: Bioinformatics for biodata analysis using Machine-Learning and network approaches

XIII Argentine Congress of Bioinformatics and Compuational Biology (XIII CAB2C) and XIII International Conference of the Iberoamerican Society of Bioinformatics (XIII SolBio)

Rosario, Argentina

2023

  • Main instructors: De Las Rivas J (CSIC-USAL-IBSAL, Spain), Hernandez-Rosales M (CINVESTAV, Mexico), Spetale F (CIFASIS- CONICET-UNR, Argentina), Navarro-Miranda M (CINVESTAV, Mexico), Alonso N (CSIC-USAL-IBSAL, Spain)
  • Red Iberoamericana de Inteligencia Artificial para Big BioData (RIABIO) and ATGenomics
  • Link: https://github.com/biocomplexnet/NetworkAnalysis

Workshop: Pangenome Analysis in Prokaryotes

2nd Summer Retreat on Bioinformatics and Complex Networks 2023

Guanajuato, Mexico

2023

Workshop: Analysis of biological and biomedical transcriptomic data using Artificial Intelligence (AI) and Machine Learning methods (ML) methods with R

ISCB-Latin America, SoIBio and BioNet MX International Conference on Bioinformatics

Querétaro, Mexico

2022

  • Main instructors: De Las Rivas J (CSIC-USAL-IBSAL, Spain), Hernandez-Rosales M (CINVESTAV, Mexico), De Las Rosa E (CSIC-USAL-IBSAL, Spain), Spetale F (CIFASIS- CONICET-UNR, Argentina), Navarro-Miranda M (CINVESTAV, Mexico)
  • Red Iberoamericana de Inteligencia Artificial para Big BioData (RIABIO)

Workshop: Introduction to python

1st Summer Retreat on Bioinformatics and Complex Networks

Michoacán, Mexico

2022

  • Main instructors: Ramírez-Rafael JA, Navarro-Miranda M
  • Bioinformatics and Complex Networks Group, CINVESTAV and ATGenomics

Workshop: Exploring Biological Data with Pandas

2nd Women in Bioinformatics & Data Science LA Conference (WBDSLA)

Virtual event, International

2021

  • Main instructors: Navarro-Miranda M, Maya O, Flores V, Mendoza-Monzoy DL
  • ATGenomics

Workshop: RStudio Beginners Tour

RLadies Cuernavaca

Virtual event, Morelos, Mexico

2021

Term course: Computational Genomics Laboratory Assistant

Facultad de Ciencias, Licenciatura en Ciencias de la Computación, UNAM

Mexico City, Mexico

2021 - 2020

  • Main instructors: Hernández-López S, Hernández D, Navarro-Miranda M
  • Description: Conducting molecular biology lectures, leading practical sessions on Bash command line and Python for NGS data analysis, organizing seminars with guest speakers on genomics applications, and supervising final projects
  • Link: https://sites.google.com/site/genomicaciencias/

Term course: Bioinformatics Practical Workshop

Graduate program in Biological Sciences, UNAM

Virtual event, Mexico City, Mexico

2021 - 2020

  • Main instructors: Mastretta-Yanez A, Truong C, Navarro-Miranda M
  • Description: Conducting practical lectures on bioinformatics, leading practical sessions on R, organizing seminars with guest speakers, and evaluating final projects
  • Link: https://github.com/AliciaMstt/TallerBioinf

Workshop: Introduction to Bioinformatics

Laboratory of Molecular and Experimental Evolution, Institute of Ecology, UNAM

Mexico City, Mexico

2019

Publications

Understanding the genomic basis of antagonistic pairwise interactions in microbial communities

N/A

N/A

2024

  • Navarro-Miranda M, Higareda-Alvear VM, Ramírez-Sánchez O, Hernández-Rosales M, Olmedo-Álvarez G. Understanding the genomic basis of antagonistic pairwise interactions in microbial communities (work in progress)

Meeting the Challenge of Genomic Analysis: A Collaboratively Developed Workshop for Pangenomics and Topological Data Analysis

N/A

N/A

2024

  • Contreras-Peruyero H, Guerrero-Flores S, Zirión-Martínez C, M. Mejía-Ponce PM, Navarro-Miranda M, Lovaco-Flores JA, Ibarra-Rodríguez JM, Pashkov A, Licona-Cassani C, Sélem-Mojica N. Meeting the Challenge of Genomic Analysis: A Collaboratively Developed Workshop for Pangenomics and Topological Data Analysis. Bioinformatics Advances (recommended publication with minor revisions)

Diversity of an uncommon elastic hypersaline microbial mat along a small-scale transect

N/A

N/A

2022

  • Espinosa-Asuar L, Monroy-Guzmán C, Madrigal-Trejo D, Navarro-Miranda M, Sánchez-Pérez J, Buenrostro Muñoz J, Villar J, Cifuentes Camargo JF, Kalambokidis M, Esquivel-Hernandez DA, Viladomat Jasso M, Escalante AE, Velez P, Figueroa M, Martinez-Cardenas A, Ramirez-Barahona S, Gasca-Pineda J, Eguiarte LE, Souza V. Diversity of an uncommon elastic hypersaline microbial mat along a small-scale transect. PeerJ. 2022 Jun 20;10:e13579. doi: 10.7717/peerj.13579. PMID: 35757167; PMCID: PMC9220918

Recent Differentiation of Aquatic Bacterial Communities in a Hydrological System in the Cuatro Ciénegas Basin, After a Natural Perturbation

N/A

N/A

2022

  • García-Ulloa M 2nd, Souza V, Esquivel-Hernández DA, Sánchez-Pérez J, Espinosa-Asuar L, Viladomat M, Marroquín-Rodríguez M, Navarro-Miranda M, Ruiz-Padilla J, Monroy-Guzmán C, Madrigal-Trejo D, Rosas-Barrera M, Vázquez-Rosas-Landa M, Eguiarte LE. Recent Differentiation of Aquatic Bacterial Communities in a Hydrological System in the Cuatro Ciénegas Basin, After a Natural Perturbation. Front Microbiol. 2022 Apr 28;13:825167. doi: 10.3389/fmicb.2022.825167. PMID: 35572686; PMCID: PMC9097865

The Importance of the Rare Biosphere for Astrobiological Studies and the Diversification and Resilience of Life on Earth

N/A

N/A

2020

  • Sánchez-Pérez, J., Villar, J. D., Alvarez-López, N., Águila, B., Buenrostro, J., Chino-Palomo, L. J., Navarro-Miranda, M, Cifuentes, J.F., Cruz-Cruz, A.G., Vega-Baray, B., Viladomat, M., Kalambokidis, M., Eguiarte, L.E., Souza, V. (2020). The Importance of the Rare Biosphere for Astrobiological Studies and the Diversification and Resilience of Life on Earth. https://doi.org/ 10.1007/978-3-030-46087-7_6

Honors and awards

Secretary

International Society for Computational Biology - Student Council, Regional Student Group - Mexico ( ISCB-SC, RSG-Mexico)

International

current - 2023

  • President: Lovaco-Flores JA (CINVESTAV), Secretary: Navarro-Miranda M (CINVESTAV), Faculty advisors: Sélem-Mojica N. (UNAM-CCM), Vazquez-Rosas-Landa M (UNAM-ICML)
  • Description: As Secretary of RSG-Mexico, I help organizing monthly virtual Journal Clubs on Computational Biology, draft funding proposals, and support national workshops as well as the Mexican team for the annual CAMDA challenge (Critical Assessment of Massive Data Analysis Conference). Additionally, we promote and participate in the Wikipedia/Wikidata Competition and other events coordinated by the ISCB Student Council globally

Member

Red Iberoamericana de Inteligencia Artificial para Big Biodata (RiaBio)

International

current - 2021

  • President: Tapia-Centro E, Internacional Franco-argentino de Ciencias de la Información y de Sistemas (CIFASIS-CONICET)
  • Description: As a member of the Red Iberoamericana de Inteligencia Artificial para Big Biodata (RiaBio), I actively engage in annual conferences and play a key role in organizing and leading workshops at international events

Member

CINVESTAV Irapuato Student Council (CECIG)

Guanajuato, Mexico

2024 - 2021

  • Description: As a member of the CINVESTAV Irapuato Student Council (CECIG), we serve as a liaison between the student community and the institution’s leadership, ensuring that student interests are effectively communicated. We also participate in meetings with the coordinators of both graduate programs and organize events that foster student integration and community building

Best Oral Presentation Award at the “XIII Argentine Congress of Bioinformatics and Compuational Biology (XIII CAB2C) and XIII International Conference of the Iberoamerican Society of Bioinformatics (XIII SolBio)”

Red Iberoamericana de Inteligencia Artificial para Big BioData (RIABIO), Asociación Argentina de Bioinformática y Biología Computacional, Sociedad Iberoamericana de Bioinformática (SoIBio)

Rosario, Argentina

2023

  • Navarro-Miranda M, Higareda-Alvear VM, Ramírez-Sánchez O, Hernández-Rosales M, Olmedo-Álvarez G
  • Modeling Microbial Competitive Interactions using Biosynthetic Gene Clusters (BGCs) and networks Features

2nd place at the Contest of Scientific Posters at the “III International Symposium of Bioinformatics”

Secretaría de Innovación, Ciencia y Tecnología del Estado de Morelos, Mexico

Morelos, Mexico

2018

  • Navarro-Miranda M, Grande R, Jiménez-Jacinto V, Verleyen J, Estrada K, Vega-Alvarado L, Llera-Herrera R, Yáñez-Rivera B, Sánchez-Flores A
  • Sequencing strategy and genomic analysis of the marine parasite Cymothoa exigua

3rd place at the Contest of Scientific Posters at the “XIX Short-stay Scientific Exhibition”

UNAM DGDC Program “Jóvenes Hacia la Investigación” (JHI)

Mexico City, Mexico

2014

  • Navarro-Miranda M, Calderón-Segura ME
  • Genotoxicological analysis of a keto-enol pesticide in human peripheral lymphocytes by micronucleus assay

Talks and Posters

Bioinformatics Week 2024 organized by the Institute of Neurobiology and the National Laboratory for Advanced Scientific Visualization (LAVIS)

Talk (* Presenter)

Queretaro, Mexico

2024

  • Navarro-Miranda M*, Higareda-Alvear VM, Ramírez-Sánchez O, Hernández-Rosales M, Olmedo-Álvarez G
  • Modeling Microbial Competitive Interactions using Biosynthetic Gene Clusters (BGCs) and Network Features

IV CONGRESS of the Student Section of the Bachelor’s Degree in Experimental Biology (SELBE) of the Division of Natural and Exact Sciences of the University of Guanajuato

Talk (* Presenter)

Virtual event, Guanajuato, Mexico

2024

  • Navarro-Miranda M*, Higareda-Alvear VM, Ramírez-Sánchez O, Hernández-Rosales M, Olmedo-Álvarez G
  • Understanding the genomic basis of competitive interactions in microbial communities

32nd Conference on Intelligent Systems For Molecular Biology (ISMB)

Poster (*Presenter)

Montreal, Canada

2024

  • Contreras-Peruyero H, Guerrero-Flores S, Zirión-Martínez C, M. Mejía-Ponce PM, Navarro-Miranda M, Lovaco-Flores JA, Ibarra-Rodríguez JM, Pashkov A, Licona-Cassani C, Sélem-Mojica N*****
  • Multidisciplinary Workshop on Pangenomics and Topological Data Analysis

XIII Argentine Congress of Bioinformatics and Compuational Biology (XIII CAB2C) y XIII International Conference of the Iberoamerican Society of Bioinformatics (XIII SolBio)

Talk (* Presenter)

Rosario, Argentina

2023

  • Navarro-Miranda M*, Higareda-Alvear VM, Ramírez-Sánchez O, Hernández-Rosales M, Olmedo-Álvarez G
  • Modeling Microbial Competitive Interactions using Biosynthetic Gene Clusters (BGCs) and Networks Features

International theoretical-practical course on metagenomic analysis organized by the Toribio Rodríguez University of Mendoza (UNTRM), Livestock and Biotechnology Research Institute (IGBI) and the Faculty of Zootechnical Engineering, Agribusiness and Biotechnology

Talk (* Presenter)

Virtual event, Peru

2023

  • Navarro-Miranda M*, Hernández-Rosales M, Olmedo-Álvarez G
  • Microbial ’Omics of environmental samples from Cuatro Ciénegas, Coahuila

12th International Conference on Complex Networks and their Applications

Poster (*Presenter)

Menton Riviera, France

2023

  • Navarro-Miranda M, Barceló-Antemate D, Hernández-Rosales M*****, Olmedo-Álvarez G
  • Interaction networks of a complex bacterial community revealed that different species possess distinct ecological roles but one species concentrates antagonism capacity

VII Congress of Biochemistry and Molecular Biology of Bacteria, Mexican Society of Biochemistry A.C.

Poster (*Presenter)

Guanajuato, Mexico

2023

  • Navarro-Miranda M*, Higareda-Alvear VM, Ramírez-Sánchez O, Hernández-Rosales M, Olmedo-Álvarez G
  • The Pangenome Puzzle: Decoding Ecological Roles and Taxonomic Affiliation in Microbial Community Competitive Interactions

ISCB-Latin America, SoIBio and BioNet MX International Conference on Bioinformatics

Talk (* Presenter)

Querétaro, México

2022

  • Navarro-Miranda M*, Higareda-Alvear VM, Ramírez-Sánchez O, Hernández-Rosales M, Olmedo-Álvarez G
  • Genomic profiling of bacteria for the prediction of synthetic community assembly under antagonistic interactions

Connections Across Borders

Poster (*Presenter)

Mexico City, Mexico

2022

  • Navarro-Miranda M*, Hernández-Rosales M, Olmedo-Álvarez G
  • Genomic profiling of potential synthetic communities from the phylum Bacillota

VI Congress of Biochemistry and Molecular Biology of Bacteria and XLI National Congress of Microbiology

Poster (*Presenter)

Oaxaca, Mexico

2019

  • Navarro-Miranda M*, García-Ulloa Gámiz M, Viladomat-Jasso M, Souza V
  • Characterization of local adaptation in the genus Virgibacillus through pangenomic analysis

III International Symposium of Bioinformatics

Poster (*Presenter)

Morelos, Mexico

2018

  • Navarro-Miranda M*, Grande R, Jiménez-Jacinto V, Verleyen J, Estrada K, Vega-Alvarado L, Llera-Herrera R, Yáñez-Rivera B, Sánchez-Flores A
  • Sequencing strategy and genomic analysis of the marine parasite Cymothoa exigua

International Symposium Extreme Ecosystems & Extremophile Organisms: Biodiversity, Physiology, Biochemistry & Biotechnology

Poster (*Presenter)

Morelos, Mexico

2017

  • Navarro-Miranda M*, Garibay HI, Heredia A, Negrón-Mendoza A
  • Adsorption of histidine exposed to ultraviolet radiation in the presence of aragonite (CaCO3): An experimental model for prebiotic chemistry

Congreso Preparatoriano de las Humanidades y XVIII Congreso Preparatoriano de las Ciencias, ENP 2 “Erasmo Castellanos”

Talk (* Presenter)

Mexico City, Mexico

2014

  • Navarro-Miranda M*, et al.
  • In vitro propagation of Prosthechea vitellina

XIX Short-stay Scientific Exhibition

Poster (*Presenter)

Mexico City, Mexico

2014

  • Navarro-Miranda M*, Calderón-Segura ME
  • Genotoxicological analysis of a keto-enol pesticide in human peripheral lymphocytes by micronucleus assay

Courses

Data Science using R: Machine Learning

Ramirez-Sánchez O

Virtual event

2024

  • Ramirez-Sánchez O

Pangenomics and Microbial Phylogenomics

The National Bioinformatics Node (NNB-CCG) and the Community of Software Developers in Bioinformatics (CDSB)

Morelos, Mexico

2022

  • Vinuesa Fleischmann P

Microbiome 16S

ATGenomics

Virtual event

2020

  • Maya O

Reconstruction of genomes from data type Whole Metagenome Shotgun and comparative genomics

Research Consortium of the Gulf of Mexico (CIGoM), Institute of Biotechnology (IBt), UNAM

Morelos, Mexico

2018

  • Godoy-Lozano E, Escobar-Zepeda A

Bioinformatics Tools UNIX, AWK, R, Python and Comprehensive course for the analysis of genomic and transcriptomic data

University Unit of Massive Throughput Sequencing and Bioinformatics (UUSMB), Institute of Biotechnology (IBt), UNAM

Morelos, Mexico

2018

  • Grande R, Jiménez-Jacinto V, Verleyen J, Estrada K, Vega-Alvarado L, Sánchez-Flores A

T1-NGS-E NGS: Genome Assembly and Annotation

National Node of Bioinformatics (NNB-UNAM) and the Ibero-American Society of Bioinformatics (SolBio), Center of Genomic Sciences (CCG, UNAM)

Morelos, Mexico

2017

  • Lozano Aguirre Beltrán LF

Science Communication

Web developer Intern

C3 Idea

Guanajuato, Mexico

2024

  • Fontove F, Ibarra-Rodríguez JM
  • Description: Development of web applications for the Government of Mexico City’s project Museo Virtual de Matemáticas.

Head of Organizing Comitte

Bioinformatics and Complex Networks Laboratory, Department of Genetic Engineering, CINVESTAV

Guanajuato, Mexico

2023

Talk and Workshop

Workshop “Ciencia Viva” CINVESTAV irapuato

Guanajuato, Mexico

2023 - 2021

  • Ph.D. Gabriela Olmedo-Álvarez and Ph.D. Maribel Hernández-Rosales

Talk and Workshop

Workshop “Ciencia Viva” Cuatro Ciénegas CBTA 22, CINVESTAV

Coahuila, Mexico

2023 - 2021

  • Ph.D. Gabriela Olmedo-Álvarez and Ph.D. Maribel Hernández-Rosales

Member of Organizing Comitte

Bioinformatics and Complex Networks Laboratory, Department of Genetic Engineering, CINVESTAV

Michoacán, Mexico

2022

  • 1st Summer Retreat on Bioinformatics and Complex Networks

Volunteer

Night of the Stars, UNAM

Mexico City, Mexico

2019

  • Ph.D. Antígona Segura (ICN) and Ph.D. Yilen Gómez Maqueo Chew (IA)
  • Star Visionaries: Women in Astrophysics and Astronomy

Volunteer

Third Day of Open Doors of the Institute of Biotechnology (IBt), UNAM

Morelos, Mexico

2018

  • Grande R, Jiménez-Jacinto V, Verleyen J, Estrada K, Vega-Alvarado L, Sánchez-Flores A
  • The Taco Metagenome